TB-Profiler result

Run: ERR1949954
Summary

Run ID: ERR1949954

Sample name:

Date: 31-03-2023 15:35:33

Number of reads: 135700

Percentage reads mapped: 67.25

Strain: lineage4

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
gyrA 7570 p.Ala90Val missense_variant 0.22 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
pncA 2288806 p.Ala146Thr missense_variant 0.29 pyrazinamide
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8404 p.His368Leu missense_variant 0.67
gyrA 8815 p.Val505Gly missense_variant 0.5
gyrA 9349 p.Phe683Cys missense_variant 0.67
fgd1 490851 c.69A>T synonymous_variant 0.5
mshA 576484 c.1137C>A synonymous_variant 0.6
mshA 576533 p.Gly396Ser missense_variant 0.5
rpoB 762259 p.Ile818Ser missense_variant 0.67
rpoC 763629 p.Val87Glu missense_variant 0.5
rpoC 765576 p.Val736Gly missense_variant 0.5
rpoC 765819 p.Leu817Gln missense_variant 0.5
rpoC 766461 p.Val1031Ala missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777354 p.Val376Gly missense_variant 0.4
mmpR5 779212 p.Ile75Phe missense_variant 0.5
rplC 800740 c.-69A>C upstream_gene_variant 0.25
rplC 800782 c.-27A>G upstream_gene_variant 0.22
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406121 p.Pro407His missense_variant 0.5
embR 1416394 p.Ile318Met missense_variant 0.29
embR 1416990 p.Thr120Pro missense_variant 1.0
embR 1417383 c.-36T>A upstream_gene_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168609 p.Asn668Lys missense_variant 0.67
PPE35 2169215 p.Glu466Asp missense_variant 0.33
PPE35 2170149 p.His155Leu missense_variant 0.33
Rv1979c 2223286 c.-122T>G upstream_gene_variant 0.67
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223320 c.-156T>G upstream_gene_variant 0.5
eis 2714642 p.Thr231Ala missense_variant 0.4
folC 2747423 p.Ser59Leu missense_variant 0.67
ribD 2987458 p.Val207Ala missense_variant 0.33
Rv2752c 3064526 p.Ile556Phe missense_variant 0.5
Rv2752c 3065916 p.Phe92Leu missense_variant 0.25
fbiD 3339152 p.Leu12* stop_gained 0.4
fbiD 3339181 p.Ala22Thr missense_variant 0.5
Rv3083 3448400 c.-104G>T upstream_gene_variant 0.67
whiB7 3568634 p.Pro16Thr missense_variant 0.67
whiB7 3568650 c.30C>A synonymous_variant 0.67
alr 3840408 p.Val338Glu missense_variant 0.4
alr 3841026 p.Val132Ala missense_variant 0.43
alr 3841232 c.189G>A synonymous_variant 0.4
alr 3841360 p.Thr21Ser missense_variant 0.4
alr 3841404 p.Glu6Val missense_variant 0.4
embC 4240120 c.258C>A synonymous_variant 0.67
embC 4240281 p.Val140Asp missense_variant 0.25
embC 4240325 p.Leu155Met missense_variant 0.4
embA 4243498 p.Val89Gly missense_variant 0.4
embB 4249242 p.Leu910Pro missense_variant 0.29
embB 4249801 c.3288T>A synonymous_variant 0.5
ethA 4328274 c.-801T>C upstream_gene_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338633 c.-112G>T upstream_gene_variant 0.33
gid 4407642 p.Arg187Ser missense_variant 0.33
gid 4408189 p.Glu5Ala missense_variant 0.2
Rv3083 3448500 c.-3_*1408del transcript_ablation 1.0